Sorting Permutations by Intergenic Operations

Genome Rearrangements are events that affect large stretches of genomes during evolution. Many mathematical models have been used to estimate the evolutionary distance between two genomes based on genome rearrangements. However, most of them focused on the (order of the) genes of a genome, disregard...

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Published in:	IEEE/ACM transactions on computational biology and bioinformatics Vol. 18; no. 6; pp. 2080 - 2093
Main Authors:	Oliveira, Andre Rodrigues, Jean, Geraldine, Fertin, Guillaume, Brito, Klairton Lima, Dias, Ulisses, Dias, Zanoni
Format:	Journal Article
Language:	English
Published:	United States IEEE 01.11.2021 The Institute of Electrical and Electronics Engineers, Inc. (IEEE) Institute of Electrical and Electronics Engineers
Subjects:	Algorithms Approximation Approximation algorithms Bioinformatics Computational Complexity Computer Science Data Structures and Algorithms DNA DNA Transposable Elements - genetics DNA, Intergenic - genetics Gene Rearrangement - genetics Gene sequencing Genes Genome - genetics Genome rearrangements Genomes Genomics Genomics - methods intergenic regions Mathematical analysis Mathematical models Nucleotide sequence Permutations Phylogeny reversals Sequence Analysis, DNA Sorting Transforms Transposition transpositions
ISSN:	1545-5963, 1557-9964, 1557-9964
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Abstract	Genome Rearrangements are events that affect large stretches of genomes during evolution. Many mathematical models have been used to estimate the evolutionary distance between two genomes based on genome rearrangements. However, most of them focused on the (order of the) genes of a genome, disregarding other important elements in it. Recently, researchers have shown that considering regions between each pair of genes, called intergenic regions , can enhance distance estimation in realistic data. Two of the most studied genome rearrangements are the reversal , which inverts a sequence of genes, and the transposition , which occurs when two adjacent gene sequences swap their positions inside the genome. In this work, we study the transposition distance between two genomes, but we also consider intergenic regions, a problem we name Sorting by Intergenic Transpositions. We show that this problem is NP-hard and propose two approximation algorithms, with factors 3.5 and 2.5, considering two distinct definitions for the problem. We also investigate the signed reversal and transposition distance between two genomes considering their intergenic regions. This second problem is called Sorting by Signed Intergenic Reversals and Intergenic Transpositions. We show that this problem is NP-hard and develop two approximation algorithms, with factors 3 and 2.5. We check how these algorithms behave when assigning weights for genome rearrangements. Finally, we implemented all these algorithms and tested them on real and simulated data.
AbstractList	Genome Rearrangements are events that affect large stretches of genomes during evolution. Many mathematical models have been used to estimate the evolutionary distance between two genomes based on genome rearrangements. However, most of them focused on the (order of the) genes of a genome, disregarding other important elements in it. Recently, researchers have shown that considering regions between each pair of genes, called intergenic regions , can enhance distance estimation in realistic data. Two of the most studied genome rearrangements are the reversal , which inverts a sequence of genes, and the transposition , which occurs when two adjacent gene sequences swap their positions inside the genome. In this work, we study the transposition distance between two genomes, but we also consider intergenic regions, a problem we name Sorting by Intergenic Transpositions. We show that this problem is NP-hard and propose two approximation algorithms, with factors 3.5 and 2.5, considering two distinct definitions for the problem. We also investigate the signed reversal and transposition distance between two genomes considering their intergenic regions. This second problem is called Sorting by Signed Intergenic Reversals and Intergenic Transpositions. We show that this problem is NP-hard and develop two approximation algorithms, with factors 3 and 2.5. We check how these algorithms behave when assigning weights for genome rearrangements. Finally, we implemented all these algorithms and tested them on real and simulated data. Genome Rearrangements are events that affect large stretches of genomes during evolution. Many mathematical models have been used to estimate the evolutionary distance between two genomes based on genome rearrangements. However, most of them focused on the (order of the) genes of a genome, disregarding other important elements in it. Recently, researchers have shown that considering regions between each pair of genes, called intergenic regions, can enhance distance estimation in realistic data. Two of the most studied genome rearrangements are the reversal, which inverts a sequence of genes, and the transposition, which occurs when two adjacent gene sequences swap their positions inside the genome. In this work, we study the transposition distance between two genomes, but we also consider intergenic regions, a problem we name Sorting by Intergenic Transpositions. We show that this problem is NP-hard and propose two approximation algorithms, with factors 3.5 and 2.5, considering two distinct definitions for the problem. We also investigate the signed reversal and transposition distance between two genomes considering their intergenic regions. This second problem is called Sorting by Signed Intergenic Reversals and Intergenic Transpositions. We show that this problem is NP-hard and develop two approximation algorithms, with factors 3 and 2.5. We check how these algorithms behave when assigning weights for genome rearrangements. Finally, we implemented all these algorithms and tested them on real and simulated data.Genome Rearrangements are events that affect large stretches of genomes during evolution. Many mathematical models have been used to estimate the evolutionary distance between two genomes based on genome rearrangements. However, most of them focused on the (order of the) genes of a genome, disregarding other important elements in it. Recently, researchers have shown that considering regions between each pair of genes, called intergenic regions, can enhance distance estimation in realistic data. Two of the most studied genome rearrangements are the reversal, which inverts a sequence of genes, and the transposition, which occurs when two adjacent gene sequences swap their positions inside the genome. In this work, we study the transposition distance between two genomes, but we also consider intergenic regions, a problem we name Sorting by Intergenic Transpositions. We show that this problem is NP-hard and propose two approximation algorithms, with factors 3.5 and 2.5, considering two distinct definitions for the problem. We also investigate the signed reversal and transposition distance between two genomes considering their intergenic regions. This second problem is called Sorting by Signed Intergenic Reversals and Intergenic Transpositions. We show that this problem is NP-hard and develop two approximation algorithms, with factors 3 and 2.5. We check how these algorithms behave when assigning weights for genome rearrangements. Finally, we implemented all these algorithms and tested them on real and simulated data.
Author	Jean, Geraldine Fertin, Guillaume Brito, Klairton Lima Dias, Ulisses Dias, Zanoni Oliveira, Andre Rodrigues
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Snippet	Genome Rearrangements are events that affect large stretches of genomes during evolution. Many mathematical models have been used to estimate the evolutionary...
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SubjectTerms	Algorithms Approximation Approximation algorithms Bioinformatics Computational Complexity Computer Science Data Structures and Algorithms DNA DNA Transposable Elements - genetics DNA, Intergenic - genetics Gene Rearrangement - genetics Gene sequencing Genes Genome - genetics Genome rearrangements Genomes Genomics Genomics - methods intergenic regions Mathematical analysis Mathematical models Nucleotide sequence Permutations Phylogeny reversals Sequence Analysis, DNA Sorting Transforms Transposition transpositions
Title	Sorting Permutations by Intergenic Operations
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